Hope and Harmony
by Buttered Croissant
Summary: Years pass, battles have been fought and peace has managed to stay in Equestria. For Twilight Sparkle, she knows her actions influence others, so she continues to teach the magic of friendship for others to follow upon and show themselves. But will it be enough when a new threat rises up and threatens her home, that may tear apart harmony as every pony knows it? R&R
1. Prologue

Twilight Sparkle sat before the Friendship map, conflicted.

The exhausted alicorn skimmed through the many letters sent to her by fellow allies that were all asking her the same question: what are you going to do, Princess Twilight?

Frankly, her answer was that she didn't know.

She groaned and rubbed her eyes, which had bags under them that might have been there for weeks. With the ongoing war, Twilight wasn't able to get a good night's sleep for quite some time.

And it seemed to have taken its toll on the princess. Her purple hair was disheveled, and a stray piece that continued to fall in front of her eye of the same color didn't help her mood. She was paler than usual. She rarely left her place on the throne where she answered the mass of letters that just kept growing and growing.

Twilight answered a letter from her brother. The captain of the Royal Guard told of how their enemies weren't giving up the fight, and the search for his daughter, Flurry Heart, was still underway. The writing was scrawled, probably because he was distraught and anxious and the same time. Shining Armor had many responsibilities, not unlike his sister. He told Twilight he missed her, and was looking forward to seeing her again at the next Meeting of the Council.

Twilight smiled a bit at the last part, and levitated a quill. She wrote back that she misses him too and she wishes to see him again also. With her magic, she sent it away and it dispersed in a few pink sparks.

After she did this, Twilight was reminded of her number one assistant, who was fighting battles alongside the dragon kingdom. Spike used to send Twilight's letters to Princess Celestia at the time when Twilight wasn't an alicorn. When she wasn't a princess with tedious work that always needed to be done.

When she was with her friends.

Twilight forgot about responding to the many messages, and she reminisced about the past. She remembered when she and her friends first wielded the Elements of Harmony. They defeated Nightmare Moon, bringing back Princess Luna, and Twilight Sparkle then realized how important friendship was, and how it was never wasted.

That was a long time ago.

In the present time, her five friends were somewhere else, helping in the war. The war.

Twilight didn't realize she had zoned out completely until the sound of doors opening reverberated through the throne room and brought her back to reality. She turned her head, still clouded, to the source of the loud sound. A young guard galloped in, slowing down to catch his breath. He was in front of the princess now. Twilight stepped off her throne.

"Princess Twilight," he addressed, "A letter for you."

She raised her eyebrows, wondering why this letter was being delivered directly to her. Twilight figured it must have been very important. He took a scroll from his bag, giving it to the alicorn, and Twilight lifted it from his mouth. She read the short note through her purple magic, and the sleepiness from earlier evaded her eyes.

"Miss? Is everything alright?" The guard asked.

He had a reason for asking that. Twilight Sparkle had an expression of pure astonishment and panic mixed together.

"Y...yes, everything is fine." She regained her composure, but still couldn't believe what she read.

After so many years, Flurry Heart had been found.


	2. Chapter 1

**Sorry for the delay, I was on vacation for a while.**

 **Thank you ctran03931 for your review, I actually have never watched Shingeki no Kyojin before, but it's interesting how it kind of connects to this story. ^^**

 **I hope you all enjoy!**

* * *

 _TEN YEARS AGO_

It was a beautiful morning in Ponyville.

It certainly was fine. But Twilight Sparkle, as she became more experienced as a princess, realized it was safer to not assume everything would remain fine, even on a pretty day like that day. Needless to say, it was still nice to enjoy the days like this one. The sky was a brilliant blue, and clear. A cool breeze blew steadily through Twilight's mane. The sun gleamed above, warming the air just enough around her, making it a comfortable temperature.

The town was peaceful, as well. She was sitting outside at a cafe, sipping camomile tea out of a tiny teacup, and she relished the feeling of the hot liquid trickling down her throat. Twilight relaxed her shoulders. Earlier today she greeted Pinkie Pie and Rarity, back from a quest out of Equestria. Even when dealing with princess duties, she knew it was nice to just have some time to herself.

Pony citizens milled around, sometimes the occasional creature being among them. Outsiders were slowly but surely getting accustomed to the Equestrian lifestyle, so there wasn't many skirmishes involving them.

Twilight was left alone aside from little foals asking for an autograph every so often. Her peace was broken, though, when she looked up from her tea to see a frantic guard galloping towards her. He was panting and wore a panicked expression.

Surprised, Twilight stood up and eyed him expectantly. "Is something wrong?"

The pegasus guard caught his breath, and regained his composure. "The princesses sent me to give you an urgent message."

Twilight wondered what could be so urgent that a royal guard had to give her a letter face to face. Usually there was teleportation magic involved with a message on a scroll, but maybe a reason would be explained on it.

He let the scroll unravel itself and held it up for her to read.

Twilight's eyes grew wide and she felt her heart drop as she scanned it. "Oh."

* * *

The two large doors leading to the throne room of Canterlot castle swung open, bathed in a magenta aura as Twilight hurried inside with two unicorn guards flanking her. The astronomical room usually held a certain power, because of the two alicorns who inhabited it, but now there was something ominous about it that didn't calm Twilight Sparkle's nerves a bit. She approached said alicorns, Princess Celestia and Princess Luna.

Twilight stiffened, because she could already tell something was wrong the second her eyes landed on the eldest. Celestia's wings drooped and she had a pained expression. She looked a few hundred years older than she actually was. Luna raised her head to look at the purple alicorn with a worried and tired appearance.

"Princess?" Twilight croaked.

Celestia opened her eyes, and they were glazed. "My...student."

She stood, her tall figure usually regal but now hunched over. Princess Luna rose also, and nudged her sister to keep her on her hooves. Twilight sensed that Celestia's magic was very low, which might have explained why she didn't send her faithful student the letter and why the guard broke his character and looked distraught.

Twilight intercepted her former teacher, holding her golden-footed hoof. "What happened?"

Luna answered, "We are not quite sure. This started at a time when I wasn't around. Perhaps at the courtyard?"

Celestia didn't answer. She just heaved a sigh and her eyes fluttered.

Luna tore her gaze from her sister, and locked eyes with Twilight. "About an hour ago, we received news of the abduction."

Twilight suddenly had a hard time keeping herself on her hooves.

Luna continued, "My sister was there, but obviously the kidnappers had powerful magic. Celestia came back to me very weak."

"This...is my fault," Twilight's voice was barely a whisper. She remembered the event that took place earlier at twilight, and guilt washed over her because she was the last pony that talked to Flurry Heart.

* * *

 _It was a dark night in Equestria. Countless stars twinkled above, and there was a slight breeze that blew gently through Canterlot. It wasn't a quiet night, though._

 _Excited murmurs could be heard from a rather large crowd of ponies and creatures, who were looking expectantly up at the sky. A large, full silver moon illuminated part of the blackness._

 _The noise died down when the populace looked in the direction of a golden structure, which was in the shape of a sun. A graceful figure came into view: a tall alicorn with a flowing pink, blue and green mane. Princess Celestia. After she appeared, four more alicorns arrived. Princess Luna, Princess Cadence, Princess Twilight, and the youngest, Princess Flurry Heart._

 _The crowd muttered in anticipation. Princess Celestia let her gaze fall over the audience, then she looked to Luna and nodded. The princess of the night then rose into the air, opening her wings, and she used her blue magic to lower the giant saucer in the sky. Princess Celestia then advanced into the air after her sister, and she raised the sun, brightening the sky._

 _Twilight followed the two sisters, rocketing into the sky with purple magic flowing, and a star exploded behind her._

 _Creatures and ponies alike cheered as the day began. Another Summer Sun Celebration._

 _Afterward, Twilight Sparkle drifted back down to the ground, and Flurry Heart approached her, eyes gleaming._

 _"Wow! That was amazing, auntie," Flurry said, flapping her large wings in excitement, knocking over a few unfortunate ponies in the process._

 _"Thanks, Flurry," Twilight replied, ruffling her fluffy hair. "It's always fun to do that, and this year was pretty special, considering it was the first time creatures out of Equestria came to see it."_

 _Twilight and Flurry Heart made their way out of the massive crowd, after Twilight nodded to Princess Celestia and Princess Luna in approval, and they did the same to her._

 _Both ponies walked around the tranquil parts of the city of Canterlot._

 _"How have you been, Flurry Heart?" Twilight asked the ten-year-old princess._

 _Flurry smiled, and said, "Very good, how about you?"_

 _"A little frazzled, to be honest," Twilight sighed. "With princess duties and all, things can get hectic, as you know."_

 _Twilight stopped and gazed up at the pale blue sky. "Thankfully, things have been peaceful. Oh, I should stop rambling—"_

 _Flurry and Twilight were interrupted when two ponies trotted forward. They were Starlight Glimmer and Sunburst._

 _"Hey Twilight!" Starlight greeted her former teacher, and she hugged Twilight briefly._

 _Flurry Heart and Sunburst embraced also, since they were very close. Starlight Glimmer now worked with him in the Crystal Empire, as she had more knowledge about friendship from the many teachings from Twilight. "It's good to see you, Flurry," Sunburst said happily._

 _Both pairs indulged in aimless conversation as the regular crowds of Canterlot gradually filled the streets again._

 _It then struck Twilight that she probably needed to get back to the Castle of Friendship to check on her friends. She remembered a few of them were sent on a quest to Griffenstone, and they'd probably be back by the time she arrived._

 _Twilight Sparkle turned to the group. "Sorry to cut things short, but I have to get back to Ponyville."_

 _Starlight frowned. "Is something wrong?"_

 _"Oh no," Twilight said quickly, "I was thinking that my friends would be back from their quest already, and I want to be there when they return."_

 _Starlight nodded, understanding. "Alright."_

 _Both Sunburst and Starlight Glimmer said goodbye, and walked away, disappearing into the crowd of Canterlot ponies._

 _Flurry Heart regarded Twilight. "I guess I'll see you later, Auntie Twilight." The vivacious pony gave the purple alicorn one last hug._

 _At the time, Twilight Sparkle didn't know that "later" wouldn't be tomorrow, next week, nor next month. It would be a lot longer time._

 _"Of course," Twilight responded with a smile. "Tell your mom and dad I said hello."_

 _With that being said, Twilight took off into the morning air._

* * *

The purple princess had ducked her head in shame, but Luna told her in firm tones, "Nopony expected this to happen, Twilight. It is not your fault."

Twilight lifted her head, giving Luna a grateful look. Princess Celestia still leaned against Luna, breathing heavily.

Twilight had started to shake from fatigue the first few minutes she had stood in the throne room, but now the involuntary movements were from a new emotion: anger.

"Guards!" She shouted, and a small group of five skidded to a halt beside her.

"Spread out," Twilight growled. "Look for Flurry Heart and do whatever it takes to get her back to the Crystal Empire. Go!"

The assembled party dashed out of the enormous space. Twilight narrowed her purple eyes, knowing that this might start a war in the ponies' peaceful home. Whoever did this was bound to be a villian, out to wreak havoc in Equestria. Obviously they didn't know what would happen if they messed with a certain bunch of ponies led by herself.

Twilight Sparkle looked out of one of the many stained glass windows. Sunlight streamed through it, splashing part of the room with colorful light, all the while bathing Twilight in it as well. The image was of her, a new princess of friendship. A duty rested upon her shoulders, she knew, of protecting Equestria no matter what.

Her dark expression would stay on her face for a while. She wasn't going to give up until Flurry Heart was back and safe in her home.


	3. Chapter 2

**Sorry I haven't updated in forever. Here things will start to get interesting...**

* * *

A single pale star hung high in the bright afternoon sky. A few clouds scuttled lazily across the great expanse, only to be dispersed quickly as a flash of purple jetted past.

The alicorn tore through the air at such high speeds that her past self would have been intimidated by them. It made sense, though, how she could accomplish this. After so much time and practice in the air the princess didn't have a problem with traversing through the skies rather than taking the train.

Twilight could almost smile at the thought of when she first started to use her wings, when she was self conscious about taking flight, which seemed silly, but it was just like starting anything new. But she didn't smile, and she didn't do that much anymore. She was flying over the ruins of her old town where she met her friends. Ponyville.

* * *

 _Twilight had never been more afraid for anypony in her life. Her niece, whom she'd known for so long yet seemed like such a short time, was missing. Where she had been taken, none would know or say that they knew when questioned._

 _She just wouldn't accept what others urged her to accept: Flurry was gone. Twilight knew that it couldn't be true. Along with her parent, she refused to believe it. So for the past few moons, she searched endlessly for any trace of her loved one so that the pink alicorn could be safe once again in her own home._

 _As she did this, Twilight also noticed some strange changes around Equestria. Especially her hometown. Her friends and acquaintances there seemed to be more... distant than she remembered when living there as a younger version of herself. It showed, too, in their actions. Their hoofsteps were slower, like the air they walked through was made of pudding. And their eyes. Twilight could have sworn the whites of their eyes were darker somehow._

 _No one else seemed to notice this, even when she asked them what was wrong. Everypony she questioned responded in happy tones, saying "Everything is fine!" or "Why would anything be wrong? We're all friends here!"_

 _Unfortunately because of this Twilight couldn't do anything to help them if there really was something wrong with them. So she brushed it off, telling herself that times can change and so can ponies, but it doesn't change the fact that everyone was happy and friends with each other._

 _After a few years, the Royal Guard and all others were still being sent on search parties to look for the still-gone Flurry Heart, even though deep down in each of their hearts they knew that the inevitable was the inevitable. There was no way to get her back, since they had searched for so long._

 _Of course, Twilight Sparkle never believed these lies for a second. As long as she was a protector of Equestria she would not give up. And following that promise, Twilight began to age. Not as in becoming more of an older pony, which she did, but meaning that she became more of a powerful figure of authority. She gained so much more maturity even when being as mature as she was before. She was serious, disciplined, and sharp as a tack._

 _That didn't mean she wasn't afraid still. In fact, most of the time she was overcome with feelings of terror and anxiousness. These feelings were probably due to the fact that the princess didn't sleep often. When not asleep she could do more. She could send letters to other kingdoms, keep up with updates and information, study, go out on more search parties. With everything that needed to be done, Twilight rarely thought about sleeping._

 _After a few more years, Twilight could finally notice more differences about each of the civilians around Equestria. She realized how the thought of there being something wrong with them evaded her mind years ago. For a while everything continued to run smoothly, until she was sent reports of fights beginning to break out._

 _It was surprising, but she wasn't too surprised when remembering what she was worried about a few years back. Twilight cursed to herself for pushing it away and not trusting her instincts. She realized that bad things seemed to happen when she didn't trust her instincts, and this realization caused her great anxiety for a long time._

 _She and Princess Luna ordered the Royal Guard to travel to each place to try to stop these brawls from happening. Princess Celestia was still under a strange spell, unable to think straight or say things that made sense, so Luna took on the job by staying by her sister's side at all times, which caused her to be inside Canterlot Castle at all times and to take on the responsibility of raising both the sun and the moon. Twilight once tried to convince her to let her take on one of the jobs, and Princess Luna refused, saying that Twilight is needed in other places but was thankful for her offer anyway._

 _Stopping the fights proved to be tedious and a long process. No one seemed to be themselves anymore, save for a few ponies here and there who were living in fear. The strong ones of each kingdom outside and inside of Equestria came to assist the ponies and other creatures in need, which included her friends, Spike and Ember, Thorax, and many others._

 _As the brawls turned into battles, the whole conundrum became a full-blown war between the "corrupted" and "uncorrupted", even though it was a mystery of what caused the creatures to be corrupted. Twilight felt the seriousness of the situation when being sent reports of injured and, sadly, deceased fighters. It was a challenge, fighting off ones who were once friends that are trying to kill you. Most of the time, Twilight could be found locked up in her castle, staying safe while sending letters and dealing with other things. The others insisted that the leaders of Equestria are the most important and should be protected._

 _So she was afraid. All the times before when problems arose there were ways to save everyone so that things could go back to normal, but she had no idea what to do. Twilight was overwhelmed, and oftentimes found herself wondering if her friends were ok. She hadn't received many letters from them since the beginning of the war. She wondered if they were even alive._

* * *

Shaking her head, Twilight kept her eyes up towards the direction she was going in, which was north towards Canterlot. She was thinking about the past ten years, which she always strived to not think about. She wanted to think about the present, and possibly the future, but not the past. It did no good to do that, anyway. It was already written down in history. There was no use in thinking about it when it already happened. Now, she has to think of how she can change it, and how it has already changed by the news she just recieved.

Twilight wore an expression that couldn't be read, but on the inside a storm of thoughts and emotions plagued her mind. She also had so many questions about her long lost niece, who had been found somehow.

Where was she taken? What events occurred while she was gone to that place? What torture did she have to endure?

Her chest tightened at the last question. Twilight never forgave herself for not being there to protect Flurry Heart. Because of her absence, she had been taken to who-knows-where to be tortured, enslaved, or tested on. It was horrible to think about, so Twilight pushed her worries off her train of thought for the time being. Focusing on her flight path once more, she realized how close she was to the place where she grew up as a filly.

Twilight landed quickly within the castle grounds with a loud 'thump', alerting the guards of her presence. At once, a swarm of them crowded around the princess, their sharp spears pointed in her direction. Calmly, she raised her large wings, signaling them to back away. One of the unicorn stallions stepped forward, and she was "scanned" with his dark-hued aura.

Once he nodded, most of the guards released a collective sigh, breaking their characters. Twilight saluted to them, walking briskly away with a few in tow.

"Where is Princess Luna now?" Twilight asked authoritatively as two guards appeared on either side of her figure, keeping steady pace with the princess as they approached Canterlot Castle.

"In the throne room, Princess," the Pegasus replied in a curt manner.

She nodded her thanks as an aura of magic enveloped the two enormous doors leading to the inside. As she made her way inside, she waved them off without a word. She galloped through the halls in a frantic, turning sharp corners and passing rooms until she entered the throne room.

Princess Luna glanced up at the sudden noise, and gave a small smile when noticing the purple princess. Shining Armor, still dressed in his Royal Guard uniform, was embracing his wife, Princess Cadence, while also holding another pony. He was shedding tears, and Cadence was shaking with sobs.

Twilight approached her brother and sister-in-law with hesitance, wondering if this was really happening. She found herself shuddering, her eyes glistening.

Their daughter turned toward the princess, and her eyes immediately brightened. Her parents acknowledged her too, and let Flurry Heart run to Twilight to share a hug that they hadn't shared in years.

"I'm so sorry," Twilight whispered the first thing that she wanted to say to Flurry ever since losing her.

Flurry let go of Twilight after what felt like an eternity and smiled at her. She was ten years older than the last time she saw her, and Twilight observed that she was slightly shorter than the pink princess.

"You shouldn't be sorry," Flurry replied, her large eyes fixed on her aunt.

"I should be," Twilight spoke, another tear threatening to fall. "I lost you."

"Oh Twilight," Flurry said, grinning. "I remember how caring you were. So ready to drop everything to save me if the time ever came."

"Yes?" Twilight looked at her in slight confusion.

"You thought you made a mistake, but in reality, you were a big help!"

Twilight blinked a couple times. "A big...help? What do you mean."

Flurry Heart dropped her grin, replacing it with a strange frown. "Oh, you were definitely a big help."

As Twilight remembered her instincts, she gasped in horror as she saw what was happening to Flurry Heart, as were the others in the room. Her niece became enveloped in a bright green light, her features disappearing and being revealed to be different ones of someone else.

Dark green smoke curled around what once was Flurry Heart's hooves, now replaced by ones that belonged to someone Twilight hadn't seen in over a decade.

"Queen Chrysalis?!" Twilight paled. "What are YOU doing here?"

Chrysalis smirked, showing her pearly white fangs, and stared defiantly at her. "Surprise."


End file.
